I am using the MEDIPS package for MeDIP-seq analysis where I am trying to create a custom genome for Vigna radiata (not already present in the package) and I am referring to below manual for guidance:
1. Genome file (gzipped) of V.radiata.
2. Seed file called BSgenome.Vradiata.UCSC.vr1-seed created referring to the manual (above link) section 2.2 Prepare the BSgenome data package seed file at page#4.
Now, I ran following commands:
> library(BSgenome) > forgeBSgenomeDataPkg("path/to/my/seed")
where path/to/my/seed = my actual path to seed file.
I encountered following error:
Creating package in ./BSgenome.Vradiata.UCSC.vr1
Error in fetchSequenceInfo(genome) : genome "vr1" is not supported
Here is the session information:
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final) locale:  LC_CTYPE=en_US.utf8 LC_NUMERIC=C  LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8  LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8  LC_PAPER=en_US.utf8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  MEDIPS_1.22.0 Rsamtools_1.24.0 BSgenome_1.40.1  rtracklayer_1.32.2 Biostrings_2.40.2 XVector_0.12.1  GenomicRanges_1.24.3 GenomeInfoDb_1.8.7 IRanges_2.6.1  S4Vectors_0.10.3 BiocGenerics_0.18.0 loaded via a namespace (and not attached):  DNAcopy_1.46.0 AnnotationDbi_1.34.4  zlibbioc_1.18.0 GenomicAlignments_1.8.4  BiocParallel_1.6.6 tools_3.3.1  SummarizedExperiment_1.2.3 Biobase_2.32.0  DBI_0.5-1 gtools_3.5.0  preprocessCore_1.34.0 bitops_1.0-6  RCurl_1.95-4.8 biomaRt_2.28.0  RSQLite_1.0.0 XML_3.98-1.4
I am clueless. Please help.
PS: I can provide the seed file if required; please let me know.